As long as you haven't already exceeded the room occupancy then you can wait to add your BF's mom until after you have already checked in. Once you are all checked in, add her to the reservation. She will not be able to be added to the dining plan though.
Once you have her added to the reservation, you can then book Magical Express for her as well. She obviously won't have the yellow luggage tags or a voucher booklet so if she has any checked luggage she can either pick it up herself or she can leave it. She will need to go to the ME desk at the airport and let them know how many checked bags she has and the info from her claim tickets. They will use that info to grab them and transport them for her. They will also print out a voucher for her and send her to a bus.
You just need to wait until after you yourself have checked in and then proceed to add her to everything. If you were to add her before your trip starts, then she would have to also have the same exact dining plan and tickets as the rest of you.
It is a very easy process and you should have no problems doing this. We have done this before when my brother decided to join us in the middle of a trip once. My parents added him to their reservation after checking in and then we booked ME for him. We were at a park when he arrived but he was able to just go to the front desk once he was at the resort and given a room key. We will be doing this again a month from now when I head down to WDW with my girls the day before my DH is meeting us there. As of right now he doesn't have ME booked yet but I will do that once I have checked in, added him, and then book ME for him.
